6
Water Quality and Missouri River Sediment Management

This report has documented how the bank control structures of the BSNP, the dams of the Pick-Sloan Plan, and water projects on Missouri River tributaries have transformed hydrologic and sedimentary processes in the Missouri River. As explained in detail in Chapter 2, these structures have trapped and immobilized large volumes of sediment in the river’s floodplains and behind mainstem dams, greatly reducing sediment concentrations in and volumes of sediment transported by the postregulation Missouri River. These changes have had many consequences, one of which was compromising the natural habitat of some of the river’s native bird, fish, and plant species. As explained in Chapter 4, the federal 2000/03 Biological Opinion issued under the Endangered Species Act has directed ways in which some portion of the river’s preregulation sediment regime and other conditions can be restored to improve prospects for federally listed fish (pallid sturgeon) and birds (least tern and piping plover). In Chapter 5, other alternatives for sediment management on the river were described at a general level, with the caveat that further understanding of their technical and socioeconomic viability would be required as MRRP, MRAPS, and other programs evolve and mature.

The statement of task to this committee also reflected concerns that sediment introduction, with associated phosphorus, may have detrimental effects on water quality within the river and as far away as the northern Gulf of Mexico. As described through this report, high concentrations of sediment were a natural feature of the preregulation river and important to its native species, and also important to land-building processes in parts of the Mississippi River delta. At the same time, in many settings and river

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6
Water Quality and Missouri
River Sediment Management
T
his report has documented how the bank control structures of the
BSNP, the dams of the Pick-Sloan Plan, and water projects on Mis-
souri River tributaries have transformed hydrologic and sedimentary
processes in the Missouri River. As explained in detail in Chapter 2, these
structures have trapped and immobilized large volumes of sediment in the
river’s floodplains and behind mainstem dams, greatly reducing sediment
concentrations in and volumes of sediment transported by the postregula-
tion Missouri River. These changes have had many consequences, one of
which was compromising the natural habitat of some of the river’s native
bird, fish, and plant species. As explained in Chapter 4, the federal 2000/03
Biological Opinion issued under the Endangered Species Act has directed
ways in which some portion of the river’s preregulation sediment regime
and other conditions can be restored to improve prospects for federally
listed fish (pallid sturgeon) and birds (least tern and piping plover). In
Chapter 5, other alternatives for sediment management on the river were
described at a general level, with the caveat that further understanding of
their technical and socioeconomic viability would be required as MRRP,
MRAPS, and other programs evolve and mature.
The statement of task to this committee also reflected concerns that
sediment introduction, with associated phosphorus, may have detrimental
effects on water quality within the river and as far away as the northern
Gulf of Mexico. As described through this report, high concentrations of
sediment were a natural feature of the preregulation river and important
to its native species, and also important to land-building processes in parts
of the Mississippi River delta. At the same time, in many settings and river
103

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systems across the country, sediment is recognized as a pollutant, with sig-
nificant federal and state program efforts in place to keep sediment out of
streams, rivers, and lakes. Therefore, in considering actions to reintroduce
sediment to the Missouri River, it is important to recognize the historic
sediment volumes, sources and characteristics when defining water quality
criteria and regulations for the Missouri River watershed.
In considering the full range of implications of the Corps of Engineers
habitat projects along the Missouri River, it is therefore important to un-
derstand not only provisions of the Endangered Species Act, but also provi-
sions of the Clean Water Act—especially setting water quality standards for
sediment and phosphorus concentrations.
This chapter responds to two questions in this report’s statement of
task:
• What is the significance of the Missouri River sediments to the gulf
of Mexico Hypoxia problem? (Question 2), and
• What are the key environmental and economic considerations re-
garding nutrient loads and/or contaminants in Missouri River sediment?
To what extent can such issues be addressed with management strategies?
(Question 4)
The first section of this chapter discusses potential effects of enhanced
Missouri River sediment transport and associated phosphorus loads on
hypoxia in the Gulf of Mexico. The following sections focus on setting
water quality criteria for sediments and nutrients that will be protective
of designated uses. The historical sediment and phosphorus loads in the
basin and prior to the construction of the Pick-Sloan mainstem dams are
discussed as context for setting nutrient (phosphorus) and sediment criteria
as required by the Clean Water Act. The discussion provides a logic for set-
ting of such criteria in ways that meet the requirements of the Clean Water
Act and that can be compatible with ongoing and possible future Missouri
River sediment management activities dictated in part by the Endangered
Species Act. The chapter concludes with a discussion of the need for im-
proved monitoring of sediments, nutrients, and other chemical constituents
in sediments discharged into the river.
POTENTIAL WATER QUALITY EFFECTS
IN THE GULF OF MEXICO
Northern Gulf of Mexico Hypoxia
Nitrogen and phosphorus delivered from the Atchafalaya and Mississippi
rivers to the northern Gulf of Mexico combine with conditions of tempera-

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FIGURE 6-2 Area of mid-summer bottom water hypoxia (dissolved oxygen < 2.0
Figure 6-2.eps
mg/L).
bitmap
SOURCE: Reprinted, with permission, from N.N. Rabalais, Louisiana Universities
Marine Consortium.
studies. The reader interested in additional reports and papers on nutrient
loadings across the Mississippi River basin, and northern Gulf of Mex-
ico hypoxia may wish to consult the following: Battaglin (2006), CENR
(2000), Rabalais and Turner (2001), Rabalais et al. (2002), Scavia et al.
(2003), Scavia and Donnelly (2007), and Turner et al. (2006).
Although excess nitrogen loads are responsible for the long-term in-
crease in hypoxic area, recent reports suggest that phosphorus may also
now be contributing to hypoxia, especially near the Mississippi and Atcha-
falaya river mouths in spring (USEPA, 2007). As a result, federal-led efforts
to address the problem have called for simultaneous reduction of nitrogen
and phosphorus loads (e.g., USEPA, 2007).
Among several reasons why the northern Gulf hypoxic zone has proven
to be a stubborn water quality remediation challenge is that it is affected
by factors other than Atchafalaya-Mississippi river nutrient discharges, and
that the areal extent varies from year to year. These complications make it
difficult to precisely track and verify relationships between nutrient loads
and the extent of the hypoxic zone. These issues are described in further
detail in a subsequent section of this chapter entitled “Measurements of
the Hypoxic Zone.”

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BOX 6-1
Recent Studies and Initiatives
Ongoing work of U.S. Geological Survey SPARROW water quality modeling. A
team of USGS scientists has been employing a spatially referenced regression
on watershed attributes (SPARROW) water quality model to determine spatial
patterns in nutrient yields across the Mississippi River basin (Alexander et al.,
2008). Among other findings the SPARROW studies show that a small number of
watersheds—several from the Corn Belt region and several from along the lower
Mississippi River—contribute a large percentage of the basin’s total nutrient yields.
Ongoing work supported by the National Oceanic and Atmospheric Administra-
tion’s Center for Sponsored Coastal Ocean Research. This program has sup-
ported most of the academic and federal research on the dynamics, causes, and
impacts of northern Gulf of Mexico hypoxia since 1990, and continues to support
this work. Results from these studies supported most of the oceanographic and
ecological findings in the integrated assessments conducted in 2000 and 2007 for
the Gulf of Mexico Task Force.
Report from the EPA Science Advisory Board report on Gulf Hypoxia. This ex-
tensive 2007 report summarizes and evaluates a large body of previous scientific
studies of the hypoxic zone. The report confirms the scientific consensus that
contemporary changes in the hypoxic zone are driven primarily by nutrient fluxes
from the Atchafalaya and Mississippi Rivers (USEPA, 2007). It also concluded that
at least a 45 percent reduction in both nitrogen and phosphorus fluxes would be
required to reduce the size of the hypoxic zone (ibid.).
Gulf of Mexico Task Force and Hypoxia Action Plan. The Mississippi River/Gulf of
Mexico Watershed Nutrient Task Force (Task Force) issued a 2001 “action plan”
in response to a directive in the 1998 Harmful Algal Bloom and Hypoxia Research
Control Act (P.L. 105-383; reauthorized in December 2004 as P.L. 108-456). The
Task Force issued a subsequent action plan in 2008. Both reports listed a goal
for reducing the size of the Gulf hypoxic zone to a 5-year running average of less
than 5,000 square kilometers (USEPA, 2001, 2008).
NRC Studies of Mississippi River Water Quality and the Clean Water Act. Two
separate NRC committees issued reports in 2008 and 2009 on Mississippi River
water quality issues and challenges (NRC, 2008, 2009b). The 2008 NRC report
focused on issues of water quality standards, monitoring, and interstate water
quality coordination. The 2009 report addressed the topics of initiating pollutant
control programs, alternatives for allocating nutrient load reductions, and docu-
menting the effectiveness of pollutant loading reduction strategies.
The Mississippi River Basin Healthy Watersheds Initiative sponsored by the U.S.
Department of Agriculture. The USDA’s Natural Resources Conservation Service
(NRCS) expects to provide $320 million over a four-year period to farmers in
select watersheds across the river basin to voluntarily implement conservation
practices that control nutrient runoff; improve wildlife habitat; and maintain agri-
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Nutrient Sources
Runoff of nutrients from forests, farms, open fields, urban areas, and
discharges of nutrients from industrial facilities and publicly owned treat-
ment plants across the Mississippi River basin are delivered eventually
to the Gulf of Mexico. The largest source of nitrogen and phosphorus in
Mississippi River water that is delivered to the Gulf of Mexico is from
agriculture (USEPA, 2007; Alexander et al., 2008). Nitrogen loads to the
Gulf increased significantly between the mid-1960s and the early 1980s,
and thereafter remained relatively constant with significant interannual
variations. The increase in nitrogen loading from the 1960s onward can be
attributed primarily, and almost exclusively, to increased use of nitrogen
fertilizer by row-crop agriculture (Goolsby et al., 1999). Total phosphorus
loads did not change significantly during this period. An increase in phos-
phorus occurred somewhat earlier—shortly after World War II—with the
advent of phosphorus-based detergents.
Figure 6-3 presents modeled estimates of the relative contributions of
nitrogen and phosphorus to the northern Gulf of Mexico from various
sources. The figure shows that greater than 70 percent of loadings from
both nitrogen and phosphorus emanate from agricultural sources (Alexan-
der et al., 2008).
The growth and persistence of the hypoxic zone, the nutrient loadings
that contribute to it, and management plans in response to it, are reflected
FIGURE 6-3 Sources of nutrients delivered to the Gulf of Mexico. Some other
estimates of these relative contributions (e.g., USEPA, 2007) produce somewhat
Figure 6-3.eps
different values.
bitmap
SOURCE: Data from Alexander et al., 2008.

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in several recent reports and initiatives (Box 6-1). These reports reach the
general conclusions that
1. Changes in the hypoxic area in the northern Gulf of Mexico are
primarily related to nutrient fluxes from the Mississippi and Atchafalaya
rivers.
2. Changes in the extent and duration of hypoxia today appear to be
more sensitive to inputs of nutrients than in the past.
3. There are early signs of deleterious long-term effects on living
resources.
4. Reducing the size of the hypoxic zone and improving water qual-
ity in the Mississippi River basin will require considerable reductions in
nitrogen and phosphorus loads. One estimate is that each source will need
to be reduced by at least 45 percent from the 1980-1996 average (USEPA,
2007).
MISSOURI RIVER SEDIMENT MANAGEMENT ACTIONS
AND IMPLICATIONS FOR NUTRIENT LOADINGS
This section discusses two approaches to considering whether the cur-
rent sediment management practices associated with the Corps of Engi-
neers’ Missouri River shallow water habitat projects, as well as possible
future actions, might significantly contribute to Gulf hypoxia. First, poten-
tial nutrient load increases from these SWH projects are compared to the
current Missouri River nutrient load, and to the overall load delivered by
the Mississippi River to the Gulf in order to determine the relative signifi-
cance of potential load increases.
Describing this relative change in nutrient loadings from these Missouri
River projects, in itself, does not address whether there may be an effect
on the hypoxic zone. Therefore, a second step draws upon on published
scientific literature relating changes in nutrient loads to the areal extent of
hypoxia, and evaluates the ultimate potential impact in the northern Gulf.
Corps of Engineers Shallow Water Habitat Projects
The Corps of Engineers Shallow Water Habitat projects will result in
releases of both nitrogen and phosphorus to the river because much of the
topsoil portion of the sediment disposed of in the river has been heavily
fertilized. Phosphorus loadings to the river from these projects, however,
are likely to constitute a much greater fraction of the current load than ad-
ditional nitrogen loadings. For example, the potential nitrogen load from
the Jameson Island (Missouri) restoration project (mentioned in Chapter
5) has been estimated as 0.23 percent of the 1994-2006 average loads at

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Hermann, Missouri (Jacobson et al., 2009). This is compared to the order-
of-magnitude-higher estimate for phosphorus—2.6 percent of the load at
Hermann—for the same project. In addition, the Missouri River provides
13 percent of the total nitrogen (TN) loads (9.8 percent of the nitrate load)
to the Gulf, compared to 20 percent of the total phosphorus (TP) loads (Au-
lenbach et al., 2007, as summarized in USEPA, 2007, Table 3). Therefore,
because it is unlikely that total nitrogen loads from the SWH projects will
be significant compared to current nitrogen loads transported in the Mis-
souri River, the remainder of this discussion will focus on total phosphorus.
Currently, the total phosphorus load to the Gulf is estimated to be
154,300 metric tons per year, with the contribution of the Missouri River to
this total load estimated to be between 16.8 and 20 percent (Aulenbach et
al., 2007 as summarized in USEPA, 2007, Table 3; Alexander et al., 2008).
To compare the potential contribution of phosphorus from the Corps SWH
projects, the same estimates of the total sediment volume these projects de-
liver to the river—34 million metric tons (Mt)/year—are used here as were
discussed in Chapter 5 (Jacobson et al., 2009).
The rate at which these sediments, and the associated phosphorus
within those sediments, are transported is important in determining their
downstream effects. Under most conditions, sediment settling and storage
processes in the Missouri and Mississippi River channels will attenuate the
load and spread delivery to the Gulf over a long period of time (e.g., years).
However, to arrive at an upper-bound estimate of downstream impacts, one
could make an assumption that all of this sediment is transported to the
Gulf in a single year.
If one makes this upper-bound assumption of all this sediment being
transported to the Gulf each year, and if sediment contains an average 443
mg-TP/kg of sediment with a standard deviation of 129 mg (Jacobson et al.,
2009; summary of Jameson Island restoration-related sampling identified
in CDM Federal Programs Corporation, 2007, Table 4-1), the increased
total phosphorus load to the Gulf would range between roughly 10,700
and 19,400 metric tons/year. This represents 6-12 percent of the current
phosphorus load from the Mississippi basin.
Again, and for purposes of illustration, this figure represents an upper-
bound estimate of additional phosphorus transported downstream from all
SWH construction-related sediment released into the Missouri River. Actual
values would almost assuredly be less than this estimated, upper-end range.
Potential Sediment Bypass Around Gavins Point Dam
It also is possible to estimate the potential total phosphorus load to the
Gulf resulting from moving sediment around Gavins Point Dam—an ag-
gressive, perhaps unlikely—sediment management measure (and described

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in Chapter 5). An estimated 6 million tons/year of sediment enter Lewis and
Clark Lake behind Gavins Point Dam (see Chapter 5; Coker et al., 2009).
Using the same range of phosphorus content as in the sediment from the
Jameson Island project, assume that no more than 6 million tons per year
will pass the dam, and further assume that that all this sediment moves to
the Gulf each year, then between roughly 1,900 and 3,500 metric tons/year
of phosphorus (P) would reach the Gulf each year. This represents 1-2 per-
cent of the current load delivered by the Mississippi River to the Gulf (see
Table 6-1). Similar to the assumptions for the construction-related sediment
releases above, this estimate of added loading represents an upper bound
and does not consider the role of the river channel in attenuating the load
and spreading its delivery over multiple years. Actual deliveries are highly
likely to be less than this upper-bound estimate of 1-2 percent.
To summarize, an upper-bound estimate of the increase in phosphorus
loadings to the Gulf as a result of the Corps shallow water habitat (SWH)
projects is a 6-12 percent increase (Table 6-1). Similarly, an upper-bound
estimate of the downstream deliveries of bypassing sediment around Gavins
Point Dam is that phosphorus loadings would increase total phosphorus
load by roughly 1-2 percent. Both these estimates represent upper bounds.
In reality, sediment deposition processes in the Missouri and Mississippi
river channels would reduce loads delivered to the Gulf, and actual down-
stream deliveries would be less than these values.
TABLE 6-1 Comparisons of Potential Annual Total Phosphorus (TP)
Augmentations to the Missouri River and Gulf of Mexico (values in
metric tons of TP/yr)
CURRENT AVERAGE LOAD TO GULF FROM MISSISSIPPI
RIVER BASIN: 154,000
CURRENT LOAD FROM MISSOURI RIVER: 25,536-30,400
(17-20 percent of total load to Gulf)
ESTIMATED UPPER BOUND LOADS FROM CORPS SWH PROJECTS: 10,700-19,400
(6-12 percent of total load to Gulf)
ESTIMATED UPPER BOUND LOADS FROM GAVINS POINT
DAM BYPASS: 1,900-3,500
(1-2 percent of total load to Gulf)
SOURCES: Data from Alexander et al., 2008; Aulenbach et al., 2007; Coker et al., 2009;
Jacobson et al., 2009; USEPA, 2007. See accompanying discussion in text.

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Potential Effects on Gulf Hypoxia
In addition to providing estimates of additional phosphorus loadings
from the two alternatives discussed above, a second question is whether
these increases could have a measureable effect on hypoxia. Conducting the
original research and modeling exercises necessary to address this second
question was beyond this committee’s resources and project scope. How-
ever, there are two articles that summarize research that derived response
curves that relate changes in areal extent of hypoxia to delivered phospho-
rus load (Greene et al., 2009; Scavia and Donnelly, 2007).
Given the considerable year-to-year variability in measured hypoxic
area, a significant and sustained change in delivered total phosphorus load
would be required to cause a clear and significant change in the size of the
hypoxic area. Given this significant interannual variability in measured
hypoxia, the confidence envelope model results is used as a measure of a
significant change in hypoxia. These error bounds in Figure 6-4 represent a
confidence interval of approximately plus or minus 20 percent. This figure
is thus used to represent a clear and a significant response to changes in
total phosphorus load.
One of these papers (Scavia and Donnelly, 2007) presents results from
a biophysical model that relates the areal extent of Gulf hypoxia to April-
June total phosphorus loads. The modeled response curve from this study
(Figure 6-4) suggests that reducing the areal extent of hypoxia by 20 per-
cent from the 2001-2007 average of 16,500 km2, would require a reduction
in the spring total phosphorus load of approximately 200 metric tons/day
(ibid.). The curve also suggests that significantly more than 200 metric tons/
day of phosphorus would be required if the hypoxic area is to permanently
increase by 20 percent. This is because, as shown in Figure 6-4, the hypoxic
area increases with increasing P loads, but at a decreasing rate.
A 2009 study developed a regression model relating hypoxic area to
February total phosphorus concentration in the Mississippi River (Greene
et al., 2009). That regression equation suggests that a 20 percent increase
in hypoxic area requires a 20 percent increase in river concentration of
TP above the current average of 210 μg-TP/l (Greene et al., 2009, Figure
3b)—or an increase of 42 μg-TP/l. River total phosphorus concentration is
fairly constant between February and June so the increase of 42 μg-TP/L
can be assumed to occur each of these months.
Average April-June river discharge is 33,000 m3/sec (Greene et al.,
2009). Multiplying the required change in river concentration (42 μg-TP/l)
by the discharge rate (33,000 m3/sec) results in a required TP load increase
of 122 metric tons/day. Thus, based on the models presented in the two pa-
pers, an increase of 100-200 metric tons/day in the spring load is needed to
produce a measureable change (e.g., 20 percent) in the Gulf hypoxic area.

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from the shallow water habitat projects and the bypass of sediments around
Gavins Point Dam are considerably less than the amounts of additional to-
tal phosphorus necessary to result in a distinct increase in the areal extent
of the Gulf hypoxic zone.
Measurements of the Hypoxic Zone
In addition to annual variation in nutrient concentrations in rivers that
discharge into the northern Gulf of Mexico, year-to-year variation in hypoxic
areal extent is controlled by several factors in addition to nutrient concentra-
tion in rivers that discharge to the Gulf. One factor is the volume of water
discharge from the Mississippi and Atchafalaya rivers; lower flows will result
in lower nutrient delivery and a smaller hypoxic zone. The areal extent of the
hypoxic zone is measured annually, in late July, by a team of scientists from
the Louisiana Universities Marine Consortium (see http://www.lumcon.edu).
The timing of this single cruise does not always coincide with the maximum
extent of the hypoxic zone in the survey year because the area of hypoxic
waters can be affected by several factors that vary from year to year. For
example, strong winds will mix the water column and temporarily aerate bot-
tom waters. Therefore, if wind mixing is particularly acute just prior to the
monitoring cruise, the measured hypoxic zone can be considerably smaller
than just prior to the major wind event, or a few weeks after the event.
Weather conditions and responsive oceanographic processes can also alter the
physical structure of the hypoxic region. For example, the areal extent of the
hypoxic zone measured in 2009 was one of the smallest recorded. However,
as explained by the science team conducting the measurements, this areal
extent was mainly a function of local weather and wind conditions:
. . . persistent winds from the west and southwest in the few weeks preced-
ing the mapping cruise likely pushed the low oxygen water mass to the
east and “piled” it up along the southeastern Louisiana shelf. The area of
hypoxia (less than 2 mg/liter), and often anoxia (no oxygen) on the eastern
part of the study area was an unusually thick layer above the bottom and
was severely low in oxygen, usually less than 0.5 mg/L. A similar situation
was documented in 1998 following persistent winds from the west, that is,
a smaller footprint but a larger volume of low oxygen (LUMCON, 2009).
Given the multiple causes of the year-to-year variation in the area of
hypoxia in the northern Gulf of Mexico, it is not appropriate to relate
discharges from select sites of relatively small nutrient loadings across the
river basin with changes in the areal extent of the hypoxic zone in any given
year. At the same time, the consensus on the role of nutrient loading from
across the river basin as a contributing factor remains, and sustained and
substantial reductions in nutrient loads from the major sub-basins are still
being recommended (e.g., USEPA, 2008).

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Available estimates of total phosphorus loads from the Corps of En-
gineers Missouri River restoration projects are small compared to current
loads from the Missouri River and the Mississippi basin. They thus appear
unlikely to influence the areal extent of the hypoxic zone. That being said,
the Corps of Engineers Missouri River restoration projects, and any ad-
ditional future projects, deliver additional nutrients to the river and Gulf
at a time that federal and state agencies, and a variety of nongovernmental
organizations, are seeking ways to reduce nutrient loadings across the Mis-
sissippi River basin.
WATER QUALITY CRITERIA
FOR SEDIMENT AND NUTRIENTS
This report does not intend to suggest that load increases of any size or
in any location can be ignored in permitting for the discharges of sediment
and nutrients into waterbodies. Increases in nutrient loads from any source,
including those that associated with sediment discharges from mitigation
and restoration projects, may have to be avoided or mitigated if avoid-
ance would be counter to meeting sediment-enrichment objectives for the
Missouri River. In fact, under current EPA guidelines for setting nutrient
criteria, “downstream” effects may need to be recognized in setting nutri-
ent criteria for discharges to the Missouri River mainstem. This section
discusses the setting of water quality criteria for nutrients.
Clean Water Act (CWA) Section 303(c) requires states to develop wa-
ter quality standards that include designated uses of waterbodies, water
quality criteria that are necessary to protect those uses, expressed in either
numeric or narrative form, and prevent waterbodies from being degraded
with reference to their current condition (antidegradation). States submit
their water quality standards to EPA for review and approval. The Missouri
Clean Water Commission, and their actions to limit discharges for sediment
to the river from Corps’ ESH and SWH restoration activities, maintained
that those activities were in violation of Missouri’s water quality standards
(see Chapter 3).
In recent years and for the specific case of nutrients, the EPA has of-
fered states guidance for development of numeric nutrient criteria. As of
2008, only one of the ten states in the Missouri River basin (Montana)
had adopted numeric criteria for nutrients. The remaining states, including
Missouri, had narrative criteria. For example, Kansas says this about total
suspended solids: “Suspended solids added to surface waters by artificial
sources shall not interfere with the behavior, reproduction, physical habi-
tat or other factors related to the survival and propagation of aquatic or
semiaquatic life or terrestrial wildlife” (Section 28-16-28e [Surface Water
Quality Criteria] of the Kansas Administrative Regulations).

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A recent EPA Inspector General report recommended the need to ac-
celerate the numeric criteria development process and focused especially on
states in the Missouri and Mississippi river basins that are large Missouri
contributors to hypoxia in the Gulf of Mexico (USEPA, 2009). Within the
basin, the EPA Region 7 supported an effort to develop guidance that would
assist the basin states in adopting numeric nutrient criteria for the shared
mainstem Missouri River. As this effort to develop numeric criteria was
underway (with limited resources), EPA actions in Florida gained national
attention. The EPA required replacing Florida’s narrative sediment and nu-
trient criteria with numeric criteria and expected such numeric criteria to be
protective of designated uses of the waterbody itself as well as downstream
waters. Clearly, the EPA effort to define numeric water quality criteria for
the Missouri River is part of an ongoing national agency effort to replace
narrative with numeric criteria that protects local and downstream waters.
Nutrient Criteria for the Missouri River
The analytical approach to developing numeric criteria has followed
well-established national EPA protocols (see Baker et al., 2008). Although
formal nutrient criteria for the Missouri River have not been proposed, the
approach being used can be summarized as follows:
• A database of nutrient chemistry on the mainstem of the Missouri
River, including the reservoirs, the channelized, and unchannelized sections,
was developed. Within these data the lower 25th percentile of TN and TP
concentrations from the general distribution of nutrient concentrations in
the water column was identified. This lower 25 percent was one method of
selecting a numeric criterion for TN and TP. However, the water column
data span a period from 1967 to the present and there are no known nutri-
ent data representing pre-dam conditions prior to 1955 when Gavins Point
Dam was closed.
• A statistical analysis was done to relate metrics characterizing ben-
thic macro-invertebrates and fish communities (such as number of species)
and chlorophyll-a concentrations to nutrients present in the water column.
Then, water column concentrations of nitrogen and phosphorus that were
associated with the ecologically best condition for the metric were identified
as possible numeric criteria. However, it is unclear from the available re-
ports what fish species were used for the fish community index and whether
those species were native fishes.
• Literature and modeling sources were used to identify conditions
that represent natural background or conditions without excessive algae,
represented by chlorophyll a measurements. These are based on the gen-
eral literature for streams (Dodds et al., 1998, 2002), and on a nationwide

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estimate of background concentrations of nutrients (Smith et al., 2003).
However, the literature does not include information for the mainstem Mis-
souri River.
The three evaluations above offer different approaches to setting nu-
trient criteria for water quality. Using these multiple lines of evidence, the
next step is to define numeric total nitrogen (TN) and total phosphorus
(TP) criteria for each major section of the Missouri River (e.g., unchannel-
ized portions of the upper Missouri, mainstem reservoirs, reaches between
reservoirs, unchannelized portions below reservoirs, and channelized por-
tions of the river). The report to EPA offered draft numeric criteria for total
nitrogen between 0.43 and 1.1 mg/l and total phosphorus between 0.05 and
0.1 mg/l for the different river segments (Missouri River Workgroup, 2008).
The application of this approach is consistent with nutrient criteria
guidance for streams in general (USEPA, 2000) and is focused on protecting
an aquatic life designated use. However, the process as applied does not
take into account the historic sediment and phosphorus conditions on the
mainstem of the Missouri river, and does not use the aquatic life that was
native to the river as the designated use. This is despite the current and fu-
ture restoration activities in the Missouri River—many of which seek to in-
crease sediment supply in the river, to better represent pre-dam conditions,
and to promote better habitat conditions for native endangered species such
as the pallid sturgeon. Given the significance of particulate phases of phos-
phorus in natural waters—and the strong correlation between phosphorus
concentrations and suspended sediment concentrations—neither can be
considered in isolation.
There also has been an independent national EPA effort to develop
approaches for the setting of numeric sediment criteria (USEPA, 2006),
although numeric sediment criteria were not the intent of the Region 7
EPA (headquartered in Kansas City) nutrient criteria development effort
described above. The specific term for sediments as a pollutant that can
cause impairment is suspended or bedded sediments (SABS) and encom-
passes suspended sediment, total suspended solids, bedload, and turbidity.
The EPA framework document is neutral about the direction of sediment
impairment; that is, the sediment numbers in a waterbody can be too low
or too high for the designated use. Also, the framework document acknowl-
edges the role of dams in severely reducing sediment supply in many rivers.
It states, for example:
Sediment starvation caused by structures such as dams and levees is a
problem in some ecosystems, ranging from the loss of native fish species
and native riparian ecosystem structure in many dammed western rivers
(e.g., Colorado River, Platte River, Missouri River) to the subsidence and
loss of wetlands (e.g., Mississippi Delta in Louisiana).

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However, the analytical approaches presented in the framework docu-
ment for future development of numeric SABS criteria are almost entirely
focused on situations where excess SABS are a cause of impairment, typi-
cally by smothering of benthic habitat or substrate needed for fish spawn-
ing. In the case of large rivers that have been dammed, and where there is
good evidence of pre- and post-dam sediment loads, the SABS framework
does not provide an analytical framework to help define criteria that rec-
ognize some level of sediments as necessary for the attainment of the
designated uses, such as along the mainstem of the Missouri River where
sediment deplention has led to bed degradation and loss of habitat for
endangered species.
Water Quality and the Historic Missouri: A Reference Condition
As discussed in previous chapters, the preregulation Missouri River
carried a substantial sediment load. And that load, as well as the nutrients
(especially phosphorus) that accompanied that load, created the conditions
that supported the native flora and fauna that characterized the Missouri
and that now are the focus of habitat and species protection and restora-
tion efforts.
Sediments as Water Quality impairments
Findings of water quality impairment due to sedimentation are com-
monplace in the U.S. and are the sixth most common cause of impairment
in waterbodies (after pathogens, metals other than mercury, mercury, nu-
trients, and organic enrichment; USEPA, 2010a). In the Missouri River
basin, there are several hundred water segments identified as impaired by
sediments, most commonly in Montana, South Dakota, and Kansas (Fig-
ure 6-5). These waters are typically smaller creeks that drain watersheds
on the order of hundreds of square miles are deemed to be impaired based,
in most instances, on narrative criteria. Frequent causes of impairment are
associated with croplands, livestock-feeding operations, grazing in riparian
lands, wastewater treatment plants, and stream bank modification.
The Missouri River basin is the site of waterbodies that are listed as im-
paired by excess sediment, and of restoration activities along the mainstem
that seek to add sediment loads to the river. These very different settings
are not necessarily in conflict and they point to the importance of recogniz-
ing that not all sediments and all rivers are the same. As was discussed in
Chapter 2, excess sediment loadings to historically clear headwater streams
can be a cause of impairment, whereas release of large grain-size sediments
to the mainstem—often being material that has been trapped by the river
control structures of the Bank Stabilization and Navigation Project over

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WATER QuAliTY AND MiSSOuRi RivER SEDiMENT MANAgEMENT
FIGURE 6-5 Missouri River basin streams that are impaired by excess sediments
and for which TMDLs have beenigure 6-5.eps
F developed.
bitmap
SOURCE: USEPA, 2010b.
the years—may be essential to attaining designated uses that support native
species.
Nutrients Associated with Sediments as Water Quality impairments
As previously discussed, phosphorus is a nutrient closely correlated
with sediment. As a result, it is likely that there were background concen-
trations of phosphorus in the Missouri River prior to the construction of
the mainstem dams and river control structures that were part of the eco-
system that supported populations of native species. However, those levels
of total phosphorus need to be estimated because direct measurements
were not conducted prior to the 1960s. No such pre-dam estimates of total
phosphorus in the Missouri River have been reported, and are estimated
below for the purpose of this discussion.
One approach to estimate historic phosphorus concentrations in the
Missouri basin is to use suspended sediment concentrations, which have

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been reported for well over a hundred years, and estimates of particulate
phosphorus concentrations from other less-developed basins. Prior to the
construction of the major dams, median sediment concentrations in the
lower Missouri River were approximately 2,000 mg/l (medians range from
1,920 mg/l to 2,330 mg/l at different stations; Blevins, 2006). More re-
cently, median concentrations are approximately 400 mg/l (456 and 378
mg/l at two stations; Blevins, 2006). Predevelopment particulate phospho-
rus concentrations (mass of phosphorus per unit mass of sediment) can be
assumed to range from 200 to 650 mg/kg, at the low end for phosphorus-
poor systems and at the high end for a basin like the Amazon (Berner
and Rao, 1994). There are reports of even higher particulate phosphorus
concentrations in less developed basins (Meybeck, 1982; Melack, 1995),
but the 200-650 mg/kg suffices for the present discussion.
In comparison, phosphorus in sediments in the Mississippi River now
average 1,085 mg/kg (Sutula et al., 2004). Using a range of 200-650 mg/
kg of particulate phosphorus to represent a range of background condi-
tions, predam background water column concentrations of 0.4-1.3 mg/l is
a reasonable estimate (assuming that the particulate forms dominate the
total phosphorus).
Phosphorus concentrations in the channelized portions of the Missouri
River today range between 0.2 and 0.6 mg/l, reflecting more phosphorus-
enriched particulates, even though the total quantity of suspended sedi-
ments is lower (Baker et al., 2008). Although there is much uncertainty
in assuming a range of phosphorus concentrations without the benefit of
historic data to calculate historic background levels, the approach em-
ployed above suggests that modern-day total phosphorus concentrations
in the lower Missouri River are not necessarily higher than the historic
background concentrations.
As another approach, a nationwide analysis of background nutrient
concentrations estimated median background total phosphorus in the
streams of the ecoregions in the Missouri River basin at approximately
0.06 mg/l (Smith et al., 2003). This approach used regressions between
land use and concentrations in small undeveloped basins as the underlying
method, and may not fully reflect the dramatic changes in sediment trans-
port regime that have occurred in the Missouri River basin. This value is
considered too low given the historic range of suspended sediments, and the
likely range of particulate phosphorus in undeveloped watersheds presented
above, but this difference does illustrate the uncertainty in understanding
the background phosphorus load in the system.
The actions of the Missouri Clean Water Commission highlight the
need for closer integration of the nutrient criteria development process and
water quality management decision making. The federal agencies, work-

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ing cooperatively with the states, can reconcile the setting of sediment
and nutrient criteria with the Endangered Species Act and congressionally
mandated programs to avoid jeopardy to three endangered species and help
restore Missouri River ecology. However, recent EPA supported water qual-
ity criteria development efforts for the mainstem Missouri were conducted
with limited time and funding and not able to fully consider the needs of
native species.
Development of numeric criteria for sediment and nutrients should be
based on further understanding of the sediment and phosphorus history
of the river, and the effects on native species, as that information becomes
available through the MRRP and other ongoing studies. The processes of
data collection, analysis, and collaboration needed to develop narrative
(and possibly numeric) criteria can require significant resources. There may
be opportunities to realize greater efficiencies and reduce resource require-
ments by incorporating the criteria development process within analyses
underway under the MRRP. The MRRIC also could help mediate disagree-
ments among federal and state agencies on proposed water quality criteria.
Sediment Releases and Water Quality Compliance
The development of narrative or numeric criteria considers historical
nutrient and sediment factors in setting limits on sediment and phosphorus
discharges to the mainstem river and as a basis for regulating such dis-
charges. However these criteria are set, regulatory consistency will require
that all sources seek to avoid making discharges, or if such discharges can-
not be avoided, offset increased loads with reductions in other places or
from other actions. Also, if there is a need for such offsets when sediment
discharges to the river are made for native species restoration, they can be
established only if there is adequate monitoring of the sediment character-
istics and the phosphorus in the sediments released. Furthermore, although
phosphorus is a key sediment-associated constituent of concern, other
chemicals of concern for water quality management are present in Missouri
River sediments in some locations. These include trace metals such as lead
and mercury, and trace organics such as PCBs and organochlorine pesticides
(Echols et al., 2008). In general, however, knowledge of total phosphorus
content or knowledge about other chemical constituents at restoration
projects is limited. The release of sediments from restoration projects, both
the total quantity and chemistry, needs to be better understood through
monitoring of construction activities in support of restoration along the
Missouri River. Knowledge of the characteristics of the sediment, as well
as concentrations of the constituents in sediment released, can be used to
judge the suitability of release of sediment into the Missouri River.

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SUMMARY
The Corps of Engineers shallow water habitat projects along the Mis-
souri River have prompted concerns about possible water quality impacts
downstream and into the northern Gulf of Mexico. As this chapter has ex-
plained, these concerns are strongly related to the development of water qual-
ity standards and nutrient criteria, historical water quality conditions of the
Missouri River, and the monitoring of sediment discharges into the Missouri.
An upper-bound estimate of the increase in phosphorus loadings to the
Gulf as a result of the Corps SWH projects is a 6-12 percent increase. Simi-
larly, an upper-bound estimate of the downstream deliveries of bypassing
sediment around Gavins Point Dam is that the additional sediment would
increase total phosphorus load by roughly 1-2 percent. Both these estimates
represent upper bounds. In reality, sediment deposition processes in the
Missouri and Mississippi River channels would reduce loads delivered to
the Gulf, and actual downstream deliveries would be less than these values.
A comparison of potential phosphorus loads from Corps SWH proj-
ects, with load increments required to produce measureable changes in the
areal extent of Gulf hypoxia, shows that these projects will not significantly
change the extent of the hypoxic area in the Gulf of Mexico. Additional
comparisons of other alternatives for reintroducing sediment to the river—
namely, bypassing sediment around Gavins Point Dam—yield a similar
conclusion that they will not significantly change the areal extent of the
hypoxic zone.
There also have been questions raised about the relationship between
loadings from the SWH projects in a given year, and possible associated
changes in the areal extent of Gulf hypoxia in the same year.
In addition to nutrient loadings, multiple factors—including meteo-
rologic, hydrodynamic, and timing factors—affect the size of the hypoxic
zone each year. Given the relatively small volumes of sediment loadings
from the Corps’ Missouri River ESH and SWH projects, it is not appropri-
ate to relate changes in the areal extent of the hypoxic zone to sediment
and nutrient loadings from Missouri River ESH and SWH projects in any
given year.
The sediment that was essential to pre-regulation river morphology and
landforms, and to the turbidity that supported the ecosystem of native spe-
cies, had certain characteristics. Development of narrative or numeric water
quality criteria that are sensitive to these historic conditions will consider
such factors in setting limits on sediment, as well as phosphorus, discharges
to the mainstem river, and as a basis for regulating such discharges. Native
species recovery objectives can be reconciled with the requirements of the
Clean Water Act by basing waterbody use designation and associated crite-
ria on aquatic life use that recognizes the needs of native species.

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The mainstem Missouri River historically carried a large sediment and
nutrient load that was important to the evolution and survival of native
flora and fauna. These pre-regulation characteristics should be considered
in the process of developing water quality standards for the Missouri River.
The federal agencies that are partners in the MRRP, and other major
Missouri River ecosystem program and initiatives, should collaborate with
ongoing EPA nutrient criteria guidance development process to achieve
agreement among themselves and with the states on designated uses for the
river, by river segment, to reflect requirements for native species. As a result
of this effort, EPA should support states that revise their existing narrative
criteria for the mainstem Missouri River in order to reflect requirements
for native species, even if such separate narrative sediment and nutrient
criteria later are replaced by numeric criteria. As appropriate, downstream
considerations (such as Gulf hypoxia) may be considered in the setting of
phosphorus criteria.
There has been a good deal of discussion regarding Corps of Engineers
habitat restoration actions along the Missouri River that introduce sediment
to the main channel. Specifically, some parties have asserted that private
entities are held to a higher standard of permitting and monitoring than a
federal agency such as the Corps of Engineers. In order to obtain better, more
systematic information on sediment dynamics along the river and specific
activities that introduce sediment, it is important that all major activities that
discharge sediment—whether private sector or governmental—be similarly
monitored and evaluated.
All actions by the Corps of Engineers that discharge sediment to the
Missouri River either during project construction or through erosion fol-
lowing construction, should be subjected to monitoring requirements for
sediment physical and chemical characteristics. This monitoring should be
conducted to ensure that sediment or other pollutants discharged to the
river comply with applicable water quality criteria.

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